Usage

After loading the kraken/2 module you can check the available databases with

$ ls $KRAKEN2_DB_PATH

Use any of the standard or custom databases we host with the '-db DBNAME' argument. E.g.

$ module load kraken/2
$ kraken2-inspect -db fungi

If you need a custom database built let us know and provide the fasta file with taxonomic IDs. We'd be happy to build and host a commonly used database.

If you get the Loading database information...classify: Error reading in hash table error, allocate more memory to the job. Keep incrementing the memory request until you see a status message in the job log like

Loading database information... done.
Processed 2488462 sequences (226450042 bp) ...